Fig. 2

Variant calling performance according to splice junction proximity, homopolymers, or allele-specific expression. n indicates the number of true variants covered by Iso-Seq data for each calculated performance measure. SNCR-SplitNCigarReads; fC-flagCorrection; DV-DeepVariant. In Clair3-based pipelines, only the pileup model was used. Performance measures for SNP (A) and indel (B) calling of sites far from (No) and near to (Yes) splice junctions for datasets Jurkat and WTC-11. C Performance measures of indel calling of sites in non-homopolymers (non-hp) and within homopolymers of a specified length; results only from WTC-11 dataset. D FN and TP rates of heterozygous SNP calling from sites in allele-specific expressed (ASE) genes and non-ASE genes; results only from WTC-11 dataset; only sites with a minimum RNA short-read coverage of 40 and minimum Iso-Seq read coverage of 20 were considered